closes #173. Improved prefix management. Requested functionality alre…

…ady exists. (#175)

CHANGELOG.rst

@@ -1,4 +1,15 @@
-Mass_Composition 0.6.5 (2024-05-18)
+Mass_Composition 0.6.7 (2024-05-19)
+===================================
+
+Feature
+-------
+
+- Improved prefix management on mc init from dataframe
+- Added cleaning code to iron_ore_met_sample_data" method in sample_data
+- No changes need to provide additional features to split_by_estimator since attr vars are already
+  passed to outputs of math operations. (#172)
+
+Mass_Composition 0.6.6 (2024-05-18)
 ===================================
 
 Feature

elphick/mass_composition/dag.py

@@ -67,6 +67,8 @@ def add_input(self, name: str) -> 'DAG':
 
     def add_step(self, name: str, operation: Callable, streams: List[str], kwargs: dict = None,
                  defined: bool = True) -> 'DAG':
+        if name in self.all_nodes_:
+            raise ValueError(f"A step with the name '{name}' already exists.")
         # Determine dependencies from the input streams
         dependencies = [self.stream_parent_node[stream] for stream in streams]
         self.graph.add_node(name, operation=operation, dependencies=dependencies, kwargs=kwargs, defined=defined)

elphick/mass_composition/datasets/sample_data.py

@@ -154,6 +154,16 @@ def iron_ore_met_sample_data() -> pd.DataFrame:
         col.strip().lower().replace(' ', '_').replace('(', '').replace(')', '').replace('%', 'pct').replace('__', '_')
         for
         col in df_met.columns]
+
+    # clean up some values and types
+    df_met = df_met.replace('-', np.nan).replace('#VALUE!', np.nan)
+    head_cols: List[str] = [col for col in df_met.columns if 'head' in col]
+    df_met[head_cols] = df_met[head_cols].astype('float64')
+    df_met['bulk_hole_no'] = df_met['bulk_hole_no'].astype('category')
+    df_met['sample_number'] = df_met['sample_number'].astype('int64')
+    df_met.set_index('sample_number', inplace=True)
+
+    # moves suffixes to prefix
     df_met = df_met.pipe(_move_suffix_to_prefix, '_head')
     df_met = df_met.pipe(_move_suffix_to_prefix, '_lump')
     return df_met

elphick/mass_composition/mass_composition.py

@@ -1,5 +1,6 @@
 import logging
 import os
+from collections import Counter
 from copy import deepcopy
 from pathlib import Path
 from typing import Dict, List, Optional, Union, Tuple, Iterable, Callable, Set, Literal, Any
@@ -75,14 +76,36 @@ def __init__(self,
         self.status: Optional[Status] = None
 
         if data is not None:
+            data = deepcopy(data)  # preserve the incoming data variable.
             self.set_data(data, constraints=constraints)
 
     @staticmethod
     def _strip_common_prefix(df: pd.DataFrame) -> Tuple[pd.DataFrame, str]:
-        common_prefix = os.path.commonprefix(df.columns.to_list())
-        stripped_df = df.copy()
-        stripped_df.columns = [col.replace(common_prefix, '') for col in df.columns]
-        return stripped_df, common_prefix
+        # Extract prefixes
+        common_prefix = MassComposition.get_common_prefix(df.columns.to_list())
+
+        res = df
+        # Create a copy of the dataframe and strip the most common prefix from column names
+        if common_prefix:
+            res = df.copy()
+            res.columns = [col.replace(common_prefix + '_', '') if col.startswith(common_prefix) else col for col in
+                           df.columns]
+
+        return res, common_prefix
+
+    @staticmethod
+    def get_common_prefix(columns: List[str]) -> str:
+        prefixes = [col.split('_')[0] for col in columns]
+        # Count the frequency of each prefix
+        prefix_counter = Counter(prefixes)
+        # Check if prefix_counter is not empty
+        if prefix_counter:
+            # Find the most common prefix
+            common_prefix, freq = prefix_counter.most_common(1)[0]
+            # Only return the prefix if its frequency is 3 or more
+            if freq >= 3:
+                return common_prefix
+        return ""
 
     def set_data(self, data: Union[pd.DataFrame, xr.Dataset],
                  constraints: Optional[Dict[str, List]] = None):
@@ -104,7 +127,8 @@ def set_data(self, data: Union[pd.DataFrame, xr.Dataset],
             # seek a prefix to self assign the name
             data, common_prefix = self._strip_common_prefix(data)
             if common_prefix:
-                self._specified_columns = {k: v.replace(common_prefix, '') for k, v in self._specified_columns.items()
+                self._specified_columns = {k: v.replace(f"{common_prefix}_", '') for k, v in
+                                           self._specified_columns.items()
                                            if v is not None}
 
             self.variables = Variables(config=self.config['vars'],
@@ -630,24 +654,24 @@ def split_by_estimator(self,
         """
         # Extract feature names from the estimator, and get the actual features
         feature_names: list[str] = list(extract_feature_names(estimator))
-        features: pd.DataFrame = self._get_features(feature_names, extra_features, allow_prefix_mismatch)
+        features: pd.DataFrame = self._get_features(feature_names, allow_prefix_mismatch=allow_prefix_mismatch,
+                                                    extra_features=extra_features)
 
         # Apply the estimator
         estimates: pd.DataFrame = estimator.predict(X=features)
         if isinstance(estimates, np.ndarray):
             raise NotImplementedError("The estimator must return a DataFrame")
 
         # Detect a possible prefix from the estimate columns
-        features_prefix: str = os.path.commonprefix(features.columns.to_list())
-        estimates_prefix: str = os.path.commonprefix(estimates.columns.to_list())
+        features_prefix: str = self.get_common_prefix(features.columns.to_list())
+        estimates_prefix: str = self.get_common_prefix(estimates.columns.to_list())
 
         # If there is a prefix, check that it matches name_1, subject to allow_prefix_mismatch
-        if estimates_prefix.strip(
-                '_') and not allow_prefix_mismatch and name_1 and not name_1 == estimates_prefix.strip('_'):
+        if estimates_prefix and not allow_prefix_mismatch and name_1 and not name_1 == estimates_prefix:
             raise ValueError(f"Common prefix mismatch: {features_prefix} and name_1: {name_1}")
 
         # assign the output names, based on specified names, allow for prefix mismatch
-        name_1 = name_1 if name_1 else estimates_prefix.strip('_')
+        name_1 = name_1 if name_1 else estimates_prefix
 
         if mass_recovery_column:
             # Transform the mass recovery to mass by applying the mass recovery to the dry mass of the input stream
@@ -661,7 +685,9 @@ def split_by_estimator(self,
                 dry_mass_var].values / mass_recovery_max
             estimates.rename(columns={mass_recovery_column: dry_mass_var}, inplace=True)
 
-        estimates.columns = [f.replace(estimates_prefix, "") for f in estimates.columns]
+        if estimates_prefix:
+            col_name_map: dict[str, str] = {f: f.replace(estimates_prefix + '_', "") for f in estimates.columns}
+            estimates.rename(columns=col_name_map, inplace=True)
 
         out: MassComposition = MassComposition(name=name_1, constraints=self.constraints, data=estimates)
         comp: MassComposition = self.sub(other=out, name=name_2)
@@ -671,7 +697,7 @@ def split_by_estimator(self,
         return out, comp
 
     def _get_features(self, feature_names: List[str], allow_prefix_mismatch: bool,
-                      extra_features: Optional[pd.DataFrame] = None,) -> pd.DataFrame:
+                      extra_features: Optional[pd.DataFrame] = None, ) -> pd.DataFrame:
         """
         This method checks if the feature names required by an estimator are present in the data. If not, it tries to
         match the feature names by considering a common prefix. If a match is found, the columns in the data are renamed
@@ -696,16 +722,16 @@ def _get_features(self, feature_names: List[str], allow_prefix_mismatch: bool,
         feature_name_map = {name.lower(): name for name in feature_names}
 
         df_features: pd.DataFrame = self.data.to_dataframe()
-        if extra_features:
+        if extra_features is not None:
             df_features = pd.concat([df_features, extra_features], axis=1)
 
         missing_features = set(f.lower() for f in feature_names) - set(c.lower() for c in df_features.columns)
 
         if missing_features:
             prefix: str = f"{self.name}_"
-            common_prefix: str = os.path.commonprefix(feature_names)
-            if common_prefix and common_prefix != prefix and allow_prefix_mismatch:
-                prefix = common_prefix
+            common_prefix: str = self.get_common_prefix(feature_names)
+            if common_prefix and common_prefix + '_' != prefix and allow_prefix_mismatch:
+                prefix = common_prefix + '_'
 
             # create a map to support renaming the columns
             prefixed_feature_map: dict[str, str] = {f: feature_name_map.get(f"{prefix}{f.lower()}") for f in

examples/504_dag_with_estimator.py

@@ -17,7 +17,6 @@
 # This import at the top to guard against the estimator extras not being installed
 from elphick.mass_composition.utils.sklearn import PandasPipeline
 
-import numpy as np
 import pandas as pd
 import plotly
 from sklearn.ensemble import RandomForestRegressor
@@ -39,18 +38,19 @@
 # ---------
 #
 # We load some metallurgical data from a drill program, REF: A072391
+# Since we are not concerned about the model performance in this example, we'll convert the categorical feature
+# bulk_hole_no to an integer
 
 df: pd.DataFrame = iron_ore_met_sample_data()
 
 base_components = ['fe', 'p', 'sio2', 'al2o3', 'loi']
-cols_x = ['dry_weight_lump_kg'] + [f'head_{comp}' for comp in base_components]
+cols_x = ['dry_weight_lump_kg'] + [f'head_{comp}' for comp in base_components] + ['bulk_hole_no']
 cols_y = ['lump_pct'] + [f'lump_{comp}' for comp in base_components]
 
-# %%
-df = df.loc[:, ['sample_number'] + cols_x + cols_y].query('lump_pct>0').replace('-', np.nan).astype(float).dropna(
-    how='any')
-df = df.rename(columns={'dry_weight_lump_kg': 'head_mass_dry'}).set_index('sample_number')
-df.index = df.index.astype(int)
+df = df.loc[:, cols_x + cols_y].query('lump_pct>0').dropna(how='any')
+df = df.rename(columns={'dry_weight_lump_kg': 'head_mass_dry'})
+df['bulk_hole_no'] = df['bulk_hole_no'].astype('category').cat.codes
+
 logger.info(df.shape)
 df.head()
 
@@ -86,40 +86,65 @@
 # ------------------------------------
 # Now we will create a MassComposition object and use it to apply the model to the feed stream.
 
-head: MassComposition = MassComposition(data=X[[col for col in X.columns if 'head' in col]],
+head: MassComposition = MassComposition(data=X_test.drop(columns=['bulk_hole_no']), name='head',
                                         mass_dry_var='head_mass_dry')
 lump, fines = head.split_by_estimator(estimator=pipe, name_2='fines',
-                                      mass_recovery_column='lump_pct', mass_recovery_max=100)
+                                      mass_recovery_column='lump_pct', mass_recovery_max=100,
+                                      extra_features=X_test['bulk_hole_no'])
+lump.data.to_dataframe().head()
 
-lump
 # %%
-fines
+fines.data.to_dataframe().head()
 
 # %%
 # Define the DAG
 # --------------
 #
-# The DAG is defined by adding nodes to the graph.  Each node is an input, output or Stream operation
-# (e.g. add, split, etc.).  The nodes are connected by the streams they operate on.
+# First we define a simple DAG, where the feed stream is split into two streams, lump and fines.
+# The lump estimator requires the usual mass-composition variables plus an addition feature/variable
+# called `bulk_hole_no`. Since the `bulk_hole_no` is available in the feed stream, it is immediately accessible
+# to the estimator.
+
+head: MassComposition = MassComposition(data=X_test, name='head',
+                                        mass_dry_var='head_mass_dry')
 
-dag = DAG(name='A072391', n_jobs=2)
+dag = DAG(name='A072391', n_jobs=1)
 dag.add_input(name='head')
 dag.add_step(name='screen', operation=Stream.split_by_estimator, streams=['head'],
              kwargs={'estimator': pipe, 'name_1': 'lump', 'name_2': 'fines',
                      'mass_recovery_column': 'lump_pct', 'mass_recovery_max': 100})
 dag.add_output(name='lump', stream='lump')
 dag.add_output(name='fines', stream='fines')
+dag.run(input_streams={'head': head}, progress_bar=True)
+
+fig = Flowsheet.from_dag(dag).plot_network()
+fig
 
 # %%
-# Run the DAG
-# -----------
+# More Complex DAG
+# ----------------
+# This DAG is to test a more complex flowsheet where the estimator may have all the features
+# immediately available in the parent stream.
 #
-# The dag is run by providing a Stream object for the input.
+# .. note::
+#    This example works, but it does so since all attribute (extra) variables are passed all the way around
+#    the network in the current design.  This is to be changed in the future to allow for more efficient processing.
+#    Once attributes are no longer passed, changes will be needed to the DAG to marshall
+#    features from other streams in the network (most often the input stream).
 
-dag.run({'head': head}, progress_bar=True)
-
-# %%
-# Create a Flowsheet object from the dag, enabling all the usual network plotting and analysis methods.
+dag = DAG(name='A072391', n_jobs=1)
+dag.add_input(name='head')
+dag.add_step(name='screen', operation=Stream.split_by_estimator, streams=['head'],
+             kwargs={'estimator': pipe, 'name_1': 'lump', 'name_2': 'fines',
+                     'mass_recovery_column': 'lump_pct', 'mass_recovery_max': 100})
+dag.add_step(name='screen_2', operation=Stream.split_by_estimator, streams=['fines'],
+             kwargs={'estimator': pipe, 'name_1': 'lump_2', 'name_2': 'fines_2',
+                     'mass_recovery_column': 'lump_pct', 'mass_recovery_max': 100,
+                     'allow_prefix_mismatch': True})
+dag.add_output(name='lump', stream='lump_2')
+dag.add_output(name='fines', stream='fines_2')
+dag.add_output(name='stockpile', stream='lump')
+dag.run(input_streams={'head': head}, progress_bar=True)
 
 fs: Flowsheet = Flowsheet.from_dag(dag)
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mass-composition"
-version = "0.6.6"
+version = "0.6.7"
 description = "For managing multi-dimensional mass-composition datasets, supporting weighted mathematical operations and visualisation."
 authors = ["Greg <greg@elphick.com.au>"]
 packages = [{ include = "elphick/mass_composition" }]

tests/test_names.py

@@ -11,4 +11,4 @@ def test_names(demo_data):
     xr_data: xr.Dataset = obj_mc._data
     df_export: pd.DataFrame = xr_data.mc.to_dataframe(original_column_names=True)
     for col in demo_data.columns:
-        assert col in list(df_export.columns), f'{col} is not in {list(demo_data.columns)}'
+        assert col in df_export.columns.to_list(), f'{col} is not in {demo_data.columns.to_list()}'